4-51995293-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001024611.3(LRRC66):c.1729G>T(p.Asp577Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D577V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001024611.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC66 | NM_001024611.3 | c.1729G>T | p.Asp577Tyr | missense_variant | 5/5 | ENST00000682860.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC66 | ENST00000682860.1 | c.1729G>T | p.Asp577Tyr | missense_variant | 5/5 | NM_001024611.3 | P1 | ||
LRRC66 | ENST00000343457.3 | c.1729G>T | p.Asp577Tyr | missense_variant | 4/4 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249034Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135068
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727246
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2024 | The c.1729G>T (p.D577Y) alteration is located in exon 5 (coding exon 4) of the LRRC66 gene. This alteration results from a G to T substitution at nucleotide position 1729, causing the aspartic acid (D) at amino acid position 577 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at